SMTL ID : 4dgr.1

Influenza Subtype 9 Neuraminidase Benzoic Acid Inhibitor Complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1: 23 residues within 4Å: Chain A: N.120, N.121, R.141 Chain C: V.242, R.248, N.250, D.251, R.284, I.286, I.288, E.295, L.297, K.309, P.310, T.311, Q.312, G.313, Q.314, F.373, L.374, G.375, Q.376 Ligands: BGC.4 6 PLIP interactions: 6 interactions with chain C Water bridges: C:E.295, C:T.311, C:Q.312, C:Q.312, C:Q.376 Hydrophobic interactions: C:F.373 Hydrogen bonds: C:G.313 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.13: 23 residues within 4Å: Chain B: N.120, N.121, R.141 Chain D: V.242, R.248, N.250, D.251, R.284, I.286, I.288, E.295, L.297, K.309, P.310, T.311, Q.312, G.313, Q.314, F.373, L.374, G.375, Q.376 Ligands: BGC.16 6 PLIP interactions: 6 interactions with chain D Water bridges: D:E.295, D:T.311, D:Q.312, D:Q.312, D:Q.376 Hydrophobic interactions: D:F.373 Hydrogen bonds: D:G.313 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.25: 23 residues within 4Å: Chain B: V.242, R.248, N.250, D.251, R.284, I.286, I.288, E.295, L.297, K.309, P.310, T.311, Q.312, G.313, Q.314, F.373, L.374, G.375, Q.376 Chain C: N.120, N.121, R.141 Ligands: BGC.28 6 PLIP interactions: 6 interactions with chain B Water bridges: B:E.295, B:T.311, B:Q.312, B:Q.312, B:Q.376 Hydrophobic interactions: B:F.373 Hydrogen bonds: B:G.313 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.37: 23 residues within 4Å: Chain A: V.242, R.248, N.250, D.251, R.284, I.286, I.288, E.295, L.297, K.309, P.310, T.311, Q.312, G.313, Q.314, F.373, L.374, G.375, Q.376 Chain D: N.120, N.121, R.141 Ligands: BGC.40 6 PLIP interactions: 6 interactions with chain A Water bridges: A:E.295, A:T.311, A:Q.312, A:Q.312, A:Q.376 Hydrophobic interactions: A:F.373 Hydrogen bonds: A:G.313

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain A: D.3, F.4, N.5, N.6, N.155 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.155 NAG-NAG.14: 5 residues within 4Å: Chain B: D.3, F.4, N.5, N.6, N.155 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.155 NAG-NAG.26: 5 residues within 4Å: Chain C: D.3, F.4, N.5, N.6, N.155 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.155 NAG-NAG.38: 5 residues within 4Å: Chain D: D.3, F.4, N.5, N.6, N.155 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.155

4 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: N.66, W.358 Chain C: Y.387 Ligands: BGC.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 4 residues within 4Å: Chain B: N.66, W.358 Chain D: Y.387 Ligands: BGC.19 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 4 residues within 4Å: Chain B: Y.387 Chain C: N.66, W.358 Ligands: BGC.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.39: 4 residues within 4Å: Chain A: Y.387 Chain D: N.66, W.358 Ligands: BGC.43 No protein-ligand interaction detected (PLIP)

12 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.4: 7 residues within 4Å: Chain A: P.118 Chain C: T.315, L.318, Q.376, W.377, D.378 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.376, C:W.377, C:D.378, C:D.378, C:D.378 BGC.6: 6 residues within 4Å: Chain A: Q.236, C.239, C.257, N.258, L.303, T.304 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.236, A:Q.236, A:Q.236, A:N.258, A:T.304 Water bridges: A:T.304, A:D.306 BGC.7: 11 residues within 4Å: Chain A: I.60, R.61, G.62, K.63, S.65, N.66, V.357, W.358, W.359, F.388 Ligands: NAG-NAG-BMA.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.61, A:S.65, A:W.359 Water bridges: A:K.63, A:N.66, A:W.358 BGC.16: 7 residues within 4Å: Chain B: P.118 Chain D: T.315, L.318, Q.376, W.377, D.378 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.13 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.376, D:W.377, D:D.378, D:D.378, D:D.378 BGC.18: 6 residues within 4Å: Chain B: Q.236, C.239, C.257, N.258, L.303, T.304 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.236, B:Q.236, B:Q.236, B:N.258, B:T.304 Water bridges: B:T.304, B:D.306 BGC.19: 11 residues within 4Å: Chain B: I.60, R.61, G.62, K.63, S.65, N.66, V.357, W.358, W.359, F.388 Ligands: NAG-NAG-BMA.15 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.61, B:S.65, B:W.359 Water bridges: B:K.63, B:N.66, B:W.358 BGC.28: 7 residues within 4Å: Chain B: T.315, L.318, Q.376, W.377, D.378 Chain C: P.118 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.25 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.376, B:W.377, B:D.378, B:D.378, B:D.378 BGC.30: 6 residues within 4Å: Chain C: Q.236, C.239, C.257, N.258, L.303, T.304 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.236, C:Q.236, C:Q.236, C:N.258, C:T.304 Water bridges: C:T.304, C:D.306 BGC.31: 11 residues within 4Å: Chain C: I.60, R.61, G.62, K.63, S.65, N.66, V.357, W.358, W.359, F.388 Ligands: NAG-NAG-BMA.27 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.61, C:S.65, C:W.359 Water bridges: C:K.63, C:N.66, C:W.358 BGC.40: 7 residues within 4Å: Chain A: T.315, L.318, Q.376, W.377, D.378 Chain D: P.118 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.37 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.376, A:W.377, A:D.378, A:D.378, A:D.378 BGC.42: 6 residues within 4Å: Chain D: Q.236, C.239, C.257, N.258, L.303, T.304 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Q.236, D:Q.236, D:Q.236, D:N.258, D:T.304 Water bridges: D:T.304, D:D.306 BGC.43: 11 residues within 4Å: Chain D: I.60, R.61, G.62, K.63, S.65, N.66, V.357, W.358, W.359, F.388 Ligands: NAG-NAG-BMA.39 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.61, D:S.65, D:W.359 Water bridges: D:K.63, D:N.66, D:W.358

4 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.5: 9 residues within 4Å: Chain A: Q.56, H.64, N.66, G.67, T.68, H.70, S.73, Y.75 Chain C: R.27 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:N.66, A:S.73, A:S.73, C:R.27, C:R.27 Water bridges: A:Q.56 Salt bridges: C:R.27 GLC.17: 9 residues within 4Å: Chain B: Q.56, H.64, N.66, G.67, T.68, H.70, S.73, Y.75 Chain D: R.27 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:R.27, D:R.27, B:N.66, B:S.73, B:S.73 Salt bridges: D:R.27 Water bridges: B:Q.56 GLC.29: 9 residues within 4Å: Chain B: R.27 Chain C: Q.56, H.64, N.66, G.67, T.68, H.70, S.73, Y.75 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:N.66, C:S.73, C:S.73, B:R.27, B:R.27 Water bridges: C:Q.56 Salt bridges: B:R.27 GLC.41: 9 residues within 4Å: Chain A: R.27 Chain D: Q.56, H.64, N.66, G.67, T.68, H.70, S.73, Y.75 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:R.27, A:R.27, D:N.66, D:S.73, D:S.73 Salt bridges: A:R.27 Water bridges: D:Q.56

4 x 3LV: 4-[2,2-bis(hydroxymethyl)-5-oxopyrrolidin-1-yl]-3-[(dipropylamino)methyl]benzoic acid(Non-covalent)

3LV.8: 18 residues within 4Å: Chain A: R.38, E.39, L.54, D.71, R.72, R.76, W.99, S.100, N.142, I.143, R.145, E.148, A.167, E.198, R.213, N.215, R.291, Y.325 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:D.71, A:R.72, A:W.99, A:I.143, A:A.167 Hydrogen bonds: A:D.71, A:R.72, A:E.148, A:E.148, A:E.198 Water bridges: A:R.213 Salt bridges: A:R.38, A:R.213, A:R.291 3LV.20: 18 residues within 4Å: Chain B: R.38, E.39, L.54, D.71, R.72, R.76, W.99, S.100, N.142, I.143, R.145, E.148, A.167, E.198, R.213, N.215, R.291, Y.325 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:D.71, B:R.72, B:W.99, B:I.143, B:A.167 Hydrogen bonds: B:D.71, B:R.72, B:E.148, B:E.148, B:E.198 Water bridges: B:R.213 Salt bridges: B:R.38, B:R.213, B:R.291 3LV.32: 18 residues within 4Å: Chain C: R.38, E.39, L.54, D.71, R.72, R.76, W.99, S.100, N.142, I.143, R.145, E.148, A.167, E.198, R.213, N.215, R.291, Y.325 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:D.71, C:R.72, C:W.99, C:I.143, C:A.167 Hydrogen bonds: C:D.71, C:R.72, C:E.148, C:E.148, C:E.198 Water bridges: C:R.213 Salt bridges: C:R.38, C:R.213, C:R.291 3LV.44: 18 residues within 4Å: Chain D: R.38, E.39, L.54, D.71, R.72, R.76, W.99, S.100, N.142, I.143, R.145, E.148, A.167, E.198, R.213, N.215, R.291, Y.325 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:D.71, D:R.72, D:W.99, D:I.143, D:A.167 Hydrogen bonds: D:D.71, D:R.72, D:E.148, D:E.148, D:E.198 Water bridges: D:R.213 Salt bridges: D:R.38, D:R.213, D:R.291

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 3 residues within 4Å: Chain A: H.70, D.71, R.72 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.71, A:D.71 Water bridges: A:R.72, A:R.72, A:R.72 Salt bridges: A:R.72 PO4.21: 3 residues within 4Å: Chain B: H.70, D.71, R.72 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.71, B:D.71 Water bridges: B:R.72, B:R.72, B:R.72 Salt bridges: B:R.72 PO4.33: 3 residues within 4Å: Chain C: H.70, D.71, R.72 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.71, C:D.71 Water bridges: C:R.72, C:R.72, C:R.72 Salt bridges: C:R.72 PO4.45: 3 residues within 4Å: Chain D: H.70, D.71, R.72 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.71, D:D.71 Water bridges: D:R.72, D:R.72, D:R.72 Salt bridges: D:R.72

8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.10: 7 residues within 4Å: Chain A: D.214, N.215, G.218, S.219, D.245, N.267, G.268 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.214, A:G.218, A:D.245, H2O.2, H2O.2 CA.11: 3 residues within 4Å: Ligands: CA.23, CA.35, CA.47 No protein-ligand interaction detected (PLIP) CA.22: 7 residues within 4Å: Chain B: D.214, N.215, G.218, S.219, D.245, N.267, G.268 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.214, B:G.218, B:D.245, H2O.19, H2O.19 CA.23: 3 residues within 4Å: Ligands: CA.11, CA.35, CA.47 No protein-ligand interaction detected (PLIP) CA.34: 7 residues within 4Å: Chain C: D.214, N.215, G.218, S.219, D.245, N.267, G.268 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.214, C:G.218, C:D.245, H2O.36, H2O.36 CA.35: 3 residues within 4Å: Ligands: CA.11, CA.23, CA.47 No protein-ligand interaction detected (PLIP) CA.46: 7 residues within 4Å: Chain D: D.214, N.215, G.218, S.219, D.245, N.267, G.268 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.214, D:G.218, D:D.245, H2O.53, H2O.54 CA.47: 3 residues within 4Å: Ligands: CA.11, CA.23, CA.35 No protein-ligand interaction detected (PLIP)

4 x K: POTASSIUM ION(Non-covalent)

K.12: 4 residues within 4Å: Chain A: E.48, C.49, D.331 Chain D: R.131 No protein-ligand interaction detected (PLIP) K.24: 4 residues within 4Å: Chain B: E.48, C.49, D.331 Chain C: R.131 No protein-ligand interaction detected (PLIP) K.36: 4 residues within 4Å: Chain A: R.131 Chain C: E.48, C.49, D.331 No protein-ligand interaction detected (PLIP) K.48: 4 residues within 4Å: Chain B: R.131 Chain D: E.48, C.49, D.331 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Venkatramani, L. et al., Crystal structure of a new benzoic acid inhibitor of influenza neuraminidase bound with a new tilt induced by overpacking sub-site C6. Bmc Struct.Biol. (2012)

Release Date

2012-05-16

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

Related Entries With Identical Sequence